Nextflow workflow report

[compassionate_meitner] (resumed run)

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 143.

The full error message was:

Error executing process > 'callVariants (1)'

Caused by:
  Process `callVariants (1)` terminated with an error exit status (143)

Command executed:

  #!/usr/bin/env bash
  
  # Convert the list into a string separated by spaces
  bedString="/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/aa/58dde70fea83f737b79d3c2d19d044/ELF3_MA0640.2_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/df/eebfd7bbaaf6f2ffd5c800806acc37/ELF1_ELF1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/0d/7441e931980abd6627c0ecf3a6bec6/TCF7L2_M08167_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ed/ca841128f4722f03ff8ca398010d7d/FOXK1_M08120_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/86/7fade0feb55034501702851c73955c/ELK4_M08112_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/52/37ea21a2c94b706309a7d5b5cc476a/ZNF786_M07721_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/cd/214d0e062bed01fa73e7bf77f946bf/PKNX1_PKNX1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/bf/c420875f5438a36765cbb0665f29b0/STAT1_STAT1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/04/ed7de03bc1129a008111579ac6c4e7/ZSCAN30_M08365_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ca/57a2e1c43017a8580ccb5d2543673d/JUN_M07836_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/cc/a9edf57b994e17818aab8f70f68c4e/TYY1_TYY1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7e/96828cb79bd071a97e2db670f41631/ZIC1_ZIC1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed 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/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/4c/ae376d789c88ae14f9556d689cbbc3/ZNF669_M07690_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c8/0fa413bbacb6bfa495d7c03d163d44/ZFP57_M07756_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/67/3d73fb1cd5d0571d0712e3320640b4/FOXA2_MA0047.3_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e9/70d32fe695254ce86f20c35470bad6/PRDM1_PRDM1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/bf/3a7842cc3bf95f46bee7a71cbb7687/FOXA1_M07962_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/62/a6a4c1e8fc0f2d0a2297ee26b404ac/KLF3_KLF3_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed 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/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f3/21ed08da62c3bab59efcf6e791d358/ZNF558_M07620_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/dd/721acbbc812f3d2cb7c9b0037a661e/ZNF41_M08245_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f3/95b8b4465e9871b278333491e5aa02/CTCF_M07918_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7b/8ee9daea383661e550504306760a7d/USF1_M07807_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5e/2d94cc551e50bc1510550c53917868/MAFF_MAFF_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ba/6810b4d7a9bc0898cc7ce190e4eb1f/PO5F1_PO5F1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/25/67d588e7260f96e960820ba89e3d4a/THAP1_M08020_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e2/3c4a959c930a3e0fc9b49b10e08111/MAX_M07795_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/00/a1f378399fefdedd98393a37afd75c/KLF5_MA0599.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/78/17934dcc5d91574a6da0146dc24dad/ZNF714_M07606_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/14/be68a2185478e398997f0aa44d90a8/ZNF716_M07664_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a5/70a6028e6108a73178bae620fab089/SOX3_SOX3_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a7/82762f12befcb9906a0d5d013a9841/ZNF263_M07844_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7a/a4ec3d7b5ca9b69f43db4dbed05317/NFKB2_NFKB2_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a9/8d6a75e6dcb949474599b7c846dbb5/ZNF613_M07646_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5f/f1c4737a9cbeac7bf5e49956fd2d8d/OVOL1_OVOL1_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/8c/0b266e56a14fc41e41cd48afddf478/ZNF846_M07707_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f8/c00c278edd5a115a50f4e3f7a5b9f2/EBF1_MA0154.4_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/cf/a32fe602185c53561eecf49066b037/SRF_M07982_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c4/e7f2c3bcf7e22f8b5640e0c9f82e75/ZSCAN29_M08271_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b5/741275ad2c5440de8769013b5376e1/ZNF467_M08260_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/07/ccaa59492693315b211d8d195f8329/MEF2C_MEF2C_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/98/935f086c7cfa6bad0bd64d9dfa7da1/JUN_M08073_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/94/445d90347540908c64bf3a087a805e/NKX21_NKX21_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b8/4f0af74c8787eced428510cdb57ac3/ZNF212_M07625_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/76/15e97bec338f63f2d1eda2b7c1dc37/BHE40_BHE40_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/fb/4221b47e22e39666cc4895ab55ff04/SP1_M08363_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/21/91f992fbfc8152b05dfce9a14a07e1/HNF6_HNF6_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/dd/3d57c5f2a6c3e15c5c5e0d1cb7ab33/FOXA1_M08117_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f9/a0feb0861872fde529536e791166c5/MXI1_M07790_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/1d/8370a8f114b36ea2022e300f65a655/CTCF_CTCF_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/4c/d0c5ea16cf550ca37a1188590a396f/FOXA2_M07959_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ce/024a32b3aca989f9de36fa7a627591/AP2C_AP2C_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f5/23627571f13f29f2f0c1eaf39b40c1/ZN816_ZN816_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5c/58daf0349baca23b2a65bf3cb64ffd/HIF1A_MA1106.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/4e/9e9f5514ea462e2962ce775efa89a7/JUND_M08067_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9b/458ad0b6ec44af869563f55bbd7597/BC11A_BC11A_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/45/2e24fc51a51047fee1ac440b69b931/FOXH1_M08119_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9b/70215122e392eb88ae3945c3f9b846/CTCF_MA1929.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f0/cbdba1f3c0628c791ed588fc737437/FOSL1_M08071_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/72/5c132e7830915ef1d307d68afffd92/ZBTB12_M08389_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e7/345482529d71985414c318d3c7350d/CEBPB_M07830_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b7/a019a0d0ad3cdc65df2c94fdd98982/YY1_M07861_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/4f/2f53a4939003e2e07979931037c19e/ZNF263_M07843_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/4a/1bf01429f24eab82ca4c0e9b80fae2/ZNF540_M07634_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/97/5991831c877f648582813636285862/ZNF341_MA1655.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/8d/b85fbe8c95b5d162e1aeaf29e7935f/ARNT_ARNT_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/51/9c065ad18625dd0bb606c19c98f94e/ZNF530_M07668_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b9/79b5c975ff8c4155d8e2b7b151b5ed/CTCF_M07911_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ac/3ddc17e7e8f59ae8e697b4b7f3a223/HNF4A_MA0114.4_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/94/8795be9ba8df757bc4d230a25554bf/ELK4_MA0076.2_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5b/c58cc8658660fb6ca73854a12194a7/HXB8_HXB8_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/91/1e726254058b155ec50934f607eab5/NRF1_NRF1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/49/e16f4e9f16cde6647c820a4cc09c29/TGIF1_TGIF1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/d1/29bac8b751d04108ae1bf7432da0b1/NFYB_M08178_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a9/481a070186b3c510a15a7a556f3d53/MAFF_M08074_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9d/e5bdf8c779af23c8a07bef9b3c4dc5/JUND_M08068_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7b/cb77f7a5e8bab3b0f20a4009961508/OTX2_OTX2_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a1/696032e31d40c528024435d6bb4f37/NKX25_NKX25_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/22/0ef27e44edf69c522f93f85323bc0a/ZNF382_MA1594.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/74/1b6deb8bfef369a4ca47a640ae7670/SPI1_M07946_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e1/a853a77c1576c2bad35f67ff4c825d/NFIL3_MA0025.2_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/27/102a2283e592e226127268ba0a526e/ZNF480_M07745_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/fa/9a67fb075949c8e18e1b55c71b15e5/EBF3_MA1637.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/0b/4269d8512e8557a3335d1837f56f65/ZNF18_M07602_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7d/cda84c52880ec934b237029561eef5/SP1_SP1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/eb/903af7814098e5ef60bf5b89190648/CTCF_M07906_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/55/6a22be1e0ebf0b4031aad88e13cf18/TFAP2C_MA0814.2_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/11/d96d6674f8bcd70e49542b8de09133/NFAC1_NFAC1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5d/2ab803622dfcdb55715b93eef87302/JUND_M07815_2.00_TOBIAS_TF_binding_sites-sorted.bed"
  
  # Split the string into an array in bash
  IFS=' ' read -r -a bedArray <<< "${bedString}"
  
  # Count number of elements in array
  echo "No. of BED files: " "${#bedArray[@]}"
  echo "First BED: " "${bedArray[0]}"
  
  mpileup_module() {
  local BEDFILES="$1"
  local BAMLIST="$2"
  local DATAID="$3"
  local FASTAFILE="$4"
  
  bash /mnt/runParallelMpileup.sh "$BEDFILES" "$BAMLIST" "$DATAID" "$FASTAFILE"
  }
  
  # export function to be used in parallel
  export -f mpileup_module
  
  # determine the number of available CPU cores
  num_cores=$(nproc)
  echo "Number of cores: "$num_cores
  
  # set arguments
  bedFileArray="${bedArray[@]}"
  bamPathList="S5F6E9K.bamlist.txt"
  dataID="S5F6E9K"
  
  # Use GNU Parallel to run the commands in parallel using all available cores
  parallel -j "$num_cores" mpileup_module ::: "${bedArray[@]}" ::: "${bamPathList}" ::: "${dataID}" ::: "/refs/GRCh38_no_alt_GCA_000001405.15.fasta"

Command exit status:
  143

Command output:
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/27/74cc7c4aad890108477e781fef758e/FOSB_FOSB_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/32/42f53547315dba68f56ae7a9b7cbb5/NFIC_M08164_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b4/7431803483a3385291d5b5b79f10f6/ZNF695_M07724_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/52/e6b04a20b039ae714b6272cd9e0e48/GTF3A_M08301_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/af/ec6e0a192573b6bfe751f201ffa3ee/ESR1_ESR1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/25/cd72dfb16c320476ac58492ca556f4/HNF4A_M08219_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/1a/abec5f47ea8f9b998808348c93fd22/BACH1_M08186_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c1/65011331c59dd7b0172608310cfc9b/ATF3_M07822_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/fa/10b8088b827565c960ae9c62b5e83e/RELA_M07999_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c5/1e556d5271b4350616f20339ca207a/STAT4_STAT4_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c8/f66ad69b0d9f3147ef5d6168badefa/ZN449_ZN449_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c4/b1e8fc5b6b84019ae68658d60bcfa8/ZNF213_M08284_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5b/cb085168152c589cc4458cfb70c060/GATA1_M07964_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/89/0902f2dab0163af078d670d15a5eb9/VDR_VDR_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c0/86363575b57d48ade4688f08c172c7/RELA_M08007_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c9/6b7bbcf4bbdc5e542591a0315f2da9/NFAC3_NFAC3_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9e/bf898a6343c595563cf214ad4943d8/GLI4_M08394_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/52/f4e3196923d994f02901d1cad6e83a/KLF8_KLF8_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/91/64d430f2879325713c0c387467dee3/GATA1_MA0035.4_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/45/64eaace4f80f683db02f0c81992ed0/ZNF200_M08232_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/eb/c8491edcdd91c5daa61744d6aafea1/ZNF680_M08343_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/13/fdbb1f6b87683b0c561dc520982bae/ATOH1_ATOH1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/92/11950e7fe10dbb147a0d68d7927740/ZNF574_M08239_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e7/7df5a1f2216da4e3973de3640003f5/FOXK1_MA0852.2_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/12/30db4eab3abc040d4c457916339ee3/KAISO_KAISO_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/30/6f876970de753a65731d599cbf2300/REST_M07849_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/2c/60f539a9adcbe66b715a52db5b8ad9/GATA1_M08202_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f5/d9f861f455f4c850ba1b362d97c0d7/TFAP4_TFAP4_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c8/c72fe4989cf4beac7dc6746027802f/IRF9_IRF9_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/8b/9fd3c55f939698b4084e78f6b19368/ZNF189_M08244_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/d2/3ba932fd3f28255aa271793a850be1/MAFF_M07839_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/01/ee38c607b5fec83a8cf38bdc692ebd/ZN547_ZN547_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/89/ba2dd680eb2c853aa4460147c58aaf/ZNF223_M07654_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b4/6052e9def8f54c5080ed1284d1b739/FOXO3_FOXO3_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/d9/578547afa65cbaf35bcecebd4b4302/ZNF140_M08372_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7a/2449ff15795903a34012092bfb0f1c/NFYB_NFYB_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/28/15eb95afa5e63e17f2a14b5ae7c424/NR2C1_NR2C1_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/be/e5d5d87f4dcaac4a15ee2ea0e903e1/MYOD1_MYOD1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/8b/6a96c6129dd192faca6f65e891201e/MXI1_M08181_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9b/6a7b2be33c5897fb2d430188e76fed/ZN335_ZN335_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f0/77534bc9202cddb61a6bdd0972001e/NFAC2_NFAC2_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/45/b47996e30c650add24af0da760bdd7/NR1I2_NR1I2_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e5/60c039e57b2be8e3c07f5758eba874/CTCF_MA0139.1_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ff/248696b9ca65f795f0a837f33ef485/REST_M07853_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/bb/061b26f5f2e5a1e34404329462df3b/ZNF433_M07726_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ef/f6dfdb0285a590ae58d74c3722ea9d/ZN708_ZN708_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c2/67d19c98f6973a9b3c750b6eabeb82/ZNF71_M08383_2.00_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/03/988743d5c3b514accb0fe94d97f575/GFI1_GFI1_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a6/53555904bf9410fdceaff4fdc0056f/TBX21_TBX21_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta
  Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/fd/dae20c43cef34038ff3e896925440e/WT1_WT1_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed S5F6E9K.bamlist.txt S5F6E9K /refs/GRCh38_no_alt_GCA_000001405.15.fasta

Command error:
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [mpileup] 16 samples in 16 input files
  [mpileup] maximum number of reads per input file set to -d 250

Work dir:
  /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/22/7629403f179b49c1c3da8ce7915629

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Run times
13-Mar-2024 18:05:57 - 14-Mar-2024 18:13:43 (duration: 1d 7m 46s)
  5 succeeded  
  1372 cached  
  0 ignored  
  1 failed  
Nextflow command
nextflow -log nextflow-logs/.nextflow.log run -resume main.nf --run_mode subset --dataset_id_list cluster-input-dir/manifests/dataset-manifest-rerun-long.txt -c nextflow_cluster.config -with-dag workflow-reports/longjobs/v2/dag-20240313-18.05.html -with-report workflow-reports/longjobs/v2/report-20240313-18.05.html -with-timeline workflow-reports/longjobs/v2/timeline-20240313-18.05.html
CPU-Hours
98.5 (1.1% cached, 24.4% failed)
Launch directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf
Work directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work
Project directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf
Script name
main.nf
Script ID
36e54b349c40c6e27d4872bf577307b1
Workflow session
4e6c7739-63ed-44aa-ad25-a94feece01e0
Workflow profile
standard
Workflow container
/home/users/ntu/suffiazi/apps/sifs/bcftools-py.sif
Container engine
singularity
Nextflow version
version 23.10.1, build 5891 (12-01-2024 22:01 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)